import jalview.structure.SequenceListener;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.ListIterator;
import java.util.Vector;
public class SeqPanel extends Panel implements MouseMotionListener,
endEditing();
if (av.getWrapAlignment())
{
- ap.scrollToWrappedVisible(seqCanvas.cursorX);
+ av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
}
else
{
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
while (seqCanvas.cursorY < ranges.getStartSeq())
{
- ap.scrollUp(true);
+ ranges.scrollUp(true);
}
- while (seqCanvas.cursorY + 1 > ranges.getEndSeq())
+ while (seqCanvas.cursorY > ranges.getEndSeq())
{
- ap.scrollUp(false);
+ ranges.scrollUp(false);
}
while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges
.getStartRes()))
{
- if (!ap.scrollRight(false))
+ if (!ranges.scrollRight(false))
{
break;
}
while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges
.getEndRes()))
{
- if (!ap.scrollRight(true))
+ if (!ranges.scrollRight(true))
{
break;
}
*
* @param sequence
* aligned sequence object
- * @param res
+ * @param column
* alignment column
* @param seq
* index of sequence in alignment
- * @return position of res in sequence
+ * @return position of column in sequence or -1 if at gap
*/
- void setStatusMessage(SequenceI sequence, int res, int seq)
+ void setStatusMessage(SequenceI sequence, int column, int seq)
{
// TODO remove duplication of identical gui method
StringBuilder text = new StringBuilder(32);
/*
* Try to translate the display character to residue name (null for gap).
*/
- final String displayChar = String.valueOf(sequence.getCharAt(res));
+ final String displayChar = String.valueOf(sequence.getCharAt(column));
if (av.getAlignment().isNucleotide())
{
residue = ResidueProperties.nucleotideName.get(displayChar);
int pos = -1;
if (residue != null)
{
- pos = sequence.findPosition(res);
+ pos = sequence.findPosition(column);
text.append(" (").append(Integer.toString(pos)).append(")");
}
av.setSelectionGroup(null);
}
- SequenceFeature[] features = findFeaturesAtRes(sequence,
- sequence.findPosition(findRes(evt)));
+ int column = findRes(evt);
+ boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+ List<SequenceFeature> features = findFeaturesAtRes(sequence,
+ sequence.findPosition(column));
+ if (isGapped)
+ {
+ removeAdjacentFeatures(features, column + 1, sequence);
+ }
- if (features != null && features.length > 0)
+ if (!features.isEmpty())
{
SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequence, features[0].getBegin(),
- features[0].getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(), features
+ .get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
- }
- if (features != null && features.length > 0)
- {
seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[] { sequence }, features, false, ap, null);
+ Collections.singletonList(sequence), features, false, ap);
seqCanvas.highlightSearchResults(null);
}
@Override
public void mouseReleased(MouseEvent evt)
{
+ boolean didDrag = mouseDragging; // did we come here after a drag
mouseDragging = false;
mouseWheelPressed = false;
- ap.paintAlignment(true);
if (!editingSeqs)
{
- doMouseReleasedDefineMode(evt);
+ doMouseReleasedDefineMode(evt, didDrag);
return;
}
{
if (av.isFollowHighlight())
{
+ // don't allow highlight of protein/cDNA to also scroll a complementary
+ // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+ // over residue to change abruptly, causing highlighted residue in panel 2
+ // to change, causing a scroll in panel 1 etc)
+ ap.setToScrollComplementPanel(false);
if (ap.scrollToPosition(results, true))
{
ap.alignFrame.repaint();
}
+ ap.setToScrollComplementPanel(true);
}
setStatusMessage(results);
seqCanvas.highlightSearchResults(results);
@Override
public void mouseMoved(MouseEvent evt)
{
- int res = findRes(evt);
+ final int column = findRes(evt);
int seq = findSeq(evt);
- if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
+ if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0)
{
if (tooltip != null)
{
}
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- if (res > sequence.getLength())
+ if (column > sequence.getLength())
{
if (tooltip != null)
{
return;
}
- int respos = sequence.findPosition(res);
- if (ssm != null)
+ final char ch = sequence.getCharAt(column);
+ boolean isGapped = Comparison.isGap(ch);
+ // find residue at column (or nearest if at a gap)
+ int respos = sequence.findPosition(column);
+
+ if (ssm != null && !isGapped)
{
- mouseOverSequence(sequence, res, respos);
+ mouseOverSequence(sequence, column, respos);
}
StringBuilder text = new StringBuilder();
text.append("Sequence ").append(Integer.toString(seq + 1))
.append(" ID: ").append(sequence.getName());
- String obj = null;
- final String ch = String.valueOf(sequence.getCharAt(res));
- if (av.getAlignment().isNucleotide())
+ if (!isGapped)
{
- obj = ResidueProperties.nucleotideName.get(ch);
- if (obj != null)
+ if (av.getAlignment().isNucleotide())
{
- text.append(" Nucleotide: ").append(obj);
+ String base = ResidueProperties.nucleotideName.get(ch);
+ text.append(" Nucleotide: ").append(base == null ? ch : base);
}
- }
- else
- {
- obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet
- .get(ch);
- if (obj != null)
+ else
{
- text.append(" Residue: ").append(obj);
+ String residue = (ch == 'x' || ch == 'X') ? "X"
+ : ResidueProperties.aa2Triplet
+ .get(String.valueOf(ch));
+ text.append(" Residue: ").append(residue == null ? ch : residue);
}
- }
-
- if (obj != null)
- {
text.append(" (").append(Integer.toString(respos)).append(")");
}
{
for (int g = 0; g < groups.length; g++)
{
- if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+ if (groups[g].getStartRes() <= column && groups[g].getEndRes() >= column)
{
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
}
}
- // use aa to see if the mouse pointer is on a
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
- sequence.findPosition(res));
-
- int index = 0;
- while (index < allFeatures.length)
+ /*
+ * add feature details to tooltip, including any that straddle
+ * a gapped position
+ */
+ if (av.isShowSequenceFeatures())
{
- SequenceFeature sf = allFeatures[index];
-
- tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
-
- if (sf.getDescription() != null)
+ List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
+ sequence.findPosition(column));
+ if (isGapped)
{
- tooltipText.append(" " + sf.getDescription());
+ removeAdjacentFeatures(allFeatures, column + 1, sequence);
}
-
- if (sf.getValue("status") != null)
+ for (SequenceFeature sf : allFeatures)
{
- String status = sf.getValue("status").toString();
- if (status.length() > 0)
+ tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
+
+ if (sf.getDescription() != null)
{
- tooltipText.append(" (" + sf.getValue("status") + ")");
+ tooltipText.append(" " + sf.getDescription());
}
- }
- tooltipText.append("\n");
- index++;
+ if (sf.getValue("status") != null)
+ {
+ String status = sf.getValue("status").toString();
+ if (status.length() > 0)
+ {
+ tooltipText.append(" (" + sf.getValue("status") + ")");
+ }
+ }
+ tooltipText.append("\n");
+ }
}
if (tooltip == null)
}
}
- SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+ /**
+ * Removes from the list of features any that start after, or end before, the
+ * given column position. This allows us to retain only those features
+ * adjacent to a gapped position that straddle the position.
+ *
+ * @param features
+ * @param column
+ * alignment column (1..)
+ * @param sequence
+ */
+ protected void removeAdjacentFeatures(List<SequenceFeature> features,
+ int column, SequenceI sequence)
{
- Vector tmp = new Vector();
+ // TODO should this be an AlignViewController method (shared by gui)?
+ ListIterator<SequenceFeature> it = features.listIterator();
+ while (it.hasNext())
+ {
+ SequenceFeature sf = it.next();
+ if (sequence.findIndex(sf.getBegin()) > column
+ || sequence.findIndex(sf.getEnd()) < column)
+ {
+ it.remove();
+ }
+ }
+ }
+
+ List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
+ {
+ List<SequenceFeature> result = new ArrayList<SequenceFeature>();
SequenceFeature[] features = sequence.getSequenceFeatures();
if (features != null)
{
if ((features[i].getBegin() <= res)
&& (features[i].getEnd() >= res))
{
- tmp.addElement(features[i]);
+ result.add(features[i]);
}
}
}
- features = new SequenceFeature[tmp.size()];
- tmp.copyInto(features);
-
- return features;
+ return result;
}
Tooltip tooltip;
fontSize = 1;
}
- av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+ av.setFont(
+ new Font(av.font.getName(), av.font.getStyle(), fontSize),
+ true);
av.setCharWidth(oldWidth);
}
else
// DETECT RIGHT MOUSE BUTTON IN AWT
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+ List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
sequence.findPosition(res));
Vector<String> links = null;
- if (allFeatures != null)
+ for (SequenceFeature sf : allFeatures)
{
- for (int i = 0; i < allFeatures.length; i++)
+ if (sf.links != null)
{
- if (allFeatures[i].links != null)
+ if (links == null)
{
- if (links == null)
- {
- links = new Vector<String>();
- }
- for (int j = 0; j < allFeatures[i].links.size(); j++)
- {
- links.addElement(allFeatures[i].links.elementAt(j));
- }
+ links = new Vector<String>();
+ }
+ for (int j = 0; j < sf.links.size(); j++)
+ {
+ links.addElement(sf.links.elementAt(j));
}
}
}
}
}
- public void doMouseReleasedDefineMode(MouseEvent evt)
+ public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
{
if (stretchGroup == null)
{
// but defer colourscheme update until hidden sequences are passed in
boolean vischange = stretchGroup.recalcConservation(true);
// here we rely on stretchGroup == av.getSelection()
- needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
+ needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
+ && afterDrag;
if (stretchGroup.cs != null)
{
stretchGroup.cs.alignmentChanged(stretchGroup,
if (mouseDragging && evt.getY() < 0
&& av.getRanges().getStartSeq() > 0)
{
- running = ap.scrollUp(true);
+ running = av.getRanges().scrollUp(true);
}
if (mouseDragging && evt.getY() >= getSize().height
&& av.getAlignment().getHeight() > av.getRanges()
.getEndSeq())
{
- running = ap.scrollUp(false);
+ running = av.getRanges().scrollUp(false);
}
if (mouseDragging && evt.getX() < 0)
{
- running = ap.scrollRight(false);
+ running = av.getRanges().scrollRight(false);
}
else if (mouseDragging && evt.getX() >= getSize().width)
{
- running = ap.scrollRight(true);
+ running = av.getRanges().scrollRight(true);
}
}
git://source.jalview.org / jalview.git / blobdiff